InfoGB is a Gameboy Emulator for the PS2. You can start games off the memory card, the USB Stick or a Hard Drive, the games are usually small enough to stroe some of them onto a MAX memory Card with a bigger Capacity like 32mb, 64mb or more.
I don't have a wii u anymore to test it myself, but if homebrews are not visible on the wii u menu I think you can press L + R + minus to open the plugin menu, there should be an option called "homebrews on wii u menu" or something similar
Or when your player dies, you can say in code, if enemy exists, do nothing, but if enemy does not exist, then create enemy at certain spot. (This would be a pain tho for lots of emeies)